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Crystal structure of MMP12 in complex with inhibitor BE4.
Analyse Crystal structure of MMP12 in complex with inhibitor BE4. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ELA
- Type
- protein
- Length
- 631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage metalloelastase
- EC
- 3.4.24.65
- UniProt
- P39900
- Ligands
- B9Z, CA, ZN
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage metalloelastase (EC 3.4.24.65) | protein | 157 | 25% helix, 17% strand | P39900 |
| B, C, D | Macrophage metalloelastase (EC 3.4.24.65) | protein | 158 | 27% helix, 17% strand | P39900 |
Ligands and binding sites
- B9Z · (2~{S})-2-[2-[4-(4-methoxyphenyl) phenyl]sulfanylphenyl]pentanedioic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 12 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- DIO · 1,4-diethylene dioxide · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.61 | 0.93 | 16 | empty |
| 2 | 159 | 0.56 | 0.81 | 25 | B9Z |
| 3 | 151 | 0.55 | 0.81 | 24 | B9Z |
| 4 | 140 | 0.54 | 0.81 | 25 | ZN, B9Z |
| 5 | 158 | 0.54 | 0.80 | 27 | B9Z |
Interfaces
4 interfaces between chains.
- A–C · 330 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 238 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6ELA · Crystal structure of MMP12 in complex with inhibitor BE4. · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P39900
- Elsewhere: RCSB PDB 6ELA · PDBe 6ELA · UniProt P39900
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